org.biojava.nbio.core.sequence.io.util

Class IOUtils

java.lang.Object

org.biojava.nbio.core.sequence.io.util.IOUtils

public class IOUtils
extends Object

Nested Class Summary

Nested Classes

Modifier and Type	Class and Description
static interface	IOUtils.ReaderProcessor Closure interface used when working with IOUtils#processReader(String).

Constructor Summary

Constructors

Constructor and Description
IOUtils()

Method Summary

Methods

Modifier and Type	Method and Description
static void	close(Closeable c) Closes any Object which implements the interface Closeable and sending any error to the logger but not forcing any explicit catching of stream errors.
static void	copy(InputStream input, OutputStream output) Moves the bytes from input to output using a 4KB byte array.
static <S extends Sequence<C>,C extends Compound> int	getGCGChecksum(List<S> sequences) Calculates GCG checksum for entire list of sequences
static <S extends Sequence<C>,C extends Compound> int	getGCGChecksum(S sequence) Calculates GCG checksum for a given sequence
static <S extends Sequence<C>,C extends Compound> String	getGCGHeader(List<S> sequences) Assembles a GCG file header
static <C extends Compound> String	getGCGType(CompoundSet<C> cs) Determines GCG type
static <S extends Sequence<C>,C extends Compound> String	getIDFormat(List<S> sequences) Creates format String for accession IDs
static List<String>	getList(BufferedReader br) Returns the contents of a buffered reader as a list of strings
static List<String>	getList(File file) Delegates to getList(InputStream) by wrapping the File in a valid stream.
static List<String>	getList(InputStream is) Delegates to getList(BufferedReader) by wrapping the InputStream in a valid reader.
static String	getPDBCharacter(boolean web, char c1, char c2, boolean similar, char c) Creates formatted String for a single character of PDB output
static String	getPDBConservation(boolean web, char c1, char c2, boolean similar) Creates formatted String for displaying conservation in PDB output
static String	getPDBLegend() Creates formatted String for displaying conservation legend in PDB output
static InputStream	openFile(File file) For a filename this code will check the extension of the file for a .gz extension.
static void	print(String string, File file) Prints string to file.
static void	processReader(BufferedReader br, IOUtils.ReaderProcessor processor) Takes in a reader and a processor, reads every line from the given file and then invokes the processor.

Methods inherited from class java.lang.Object

clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait

Constructor Detail

IOUtils

public IOUtils()

Method Detail

close

public static void close(Closeable c)

Closes any Object which implements the interface Closeable and sending any error to the logger but not forcing any explicit catching of stream errors.

Parameters:

c - The stream to close

copy

public static void copy(InputStream input,
        OutputStream output)
                 throws IOException

Moves the bytes from input to output using a 4KB byte array.

Parameters:

input - Input stream of bytes

output - Output stream of bytes

Throws:

IOException - If anything occurs in the case of the reads and writes

processReader

public static void processReader(BufferedReader br,
                 IOUtils.ReaderProcessor processor)
                          throws ParserException

Takes in a reader and a processor, reads every line from the given file and then invokes the processor. What you do with the lines is dependent on your processor. The code will automatically close the given BufferedReader.

Parameters:

br - The reader to process

processor - The processor to invoke on all lines

Throws:

ParserException - Can throw this if we cannot parse the given reader

getList

public static List<String> getList(BufferedReader br)
                            throws ParserException

Returns the contents of a buffered reader as a list of strings

Parameters:

br - BufferedReader to read from; will be closed

Returns:

List of Strings

Throws:

ParserException - Can throw this if we cannot parse the given reader

getList

public static List<String> getList(InputStream is)
                            throws ParserException

Delegates to getList(BufferedReader) by wrapping the InputStream in a valid reader. No encoding is mentioned so if you need anything more advanced then use the other version of this method.

Parameters:

is - InputStream which is a text file

Returns:

List of Strings representing the lines of the files

Throws:

ParserException - Can throw this if the file is not a file or we cannot parse it

getList

public static List<String> getList(File file)
                            throws IOException

Delegates to getList(InputStream) by wrapping the File in a valid stream. No encoding is mentioned so if you need anything more advanced then use the other version of this method. Since this uses openFile(File) this code can support GZipped and plain files.

Parameters:

file - File which is a text file

Returns:

List of Strings representing the lines of the files

Throws:

IOException

openFile

public static InputStream openFile(File file)
                            throws IOException

For a filename this code will check the extension of the file for a .gz extension. If it finds one then the InputStream given back is a GZIPInputStream. Otherwise we return a normal FileInputStream.

Parameters:

file - File which may or may not be GZipped

Returns:

The final stream

Throws:

IOExceptio - n

IOException

getGCGChecksum

public static <S extends Sequence<C>,C extends Compound> int getGCGChecksum(List<S> sequences)

Calculates GCG checksum for entire list of sequences

Parameters:

sequences - list of sequences

Returns:

GCG checksum

getGCGChecksum

public static <S extends Sequence<C>,C extends Compound> int getGCGChecksum(S sequence)

Calculates GCG checksum for a given sequence

Parameters:

sequence - given sequence

Returns:

GCG checksum

getGCGHeader

public static <S extends Sequence<C>,C extends Compound> String getGCGHeader(List<S> sequences)

Assembles a GCG file header

Parameters:

sequences - list of sequences

Returns:

GCG header

getGCGType

public static <C extends Compound> String getGCGType(CompoundSet<C> cs)

Determines GCG type

Parameters:

cs - compound set of sequences

Returns:

GCG type

getIDFormat

public static <S extends Sequence<C>,C extends Compound> String getIDFormat(List<S> sequences)

Creates format String for accession IDs

Parameters:

sequences - list of sequences

Returns:

format String for accession IDs

getPDBCharacter

public static String getPDBCharacter(boolean web,
                     char c1,
                     char c2,
                     boolean similar,
                     char c)

Creates formatted String for a single character of PDB output

Parameters:

web - true for HTML display

c1 - character in first sequence

c2 - character in second sequence

similar - true if c1 and c2 are considered similar compounds

c - character to display

Returns:

formatted String

getPDBConservation

public static String getPDBConservation(boolean web,
                        char c1,
                        char c2,
                        boolean similar)

Creates formatted String for displaying conservation in PDB output

Parameters:

web - true for HTML display

c1 - character in first sequence

c2 - character in second sequence

similar - true if c1 and c2 are considered similar compounds

Returns:

formatted String

getPDBLegend

public static String getPDBLegend()

Creates formatted String for displaying conservation legend in PDB output

Returns:

legend String

print

public static void print(String string,
         File file)
                  throws IOException

Prints string to file.

Throws:

IOException - If any I/O exception occurs while printing; this method does not catch any exceptions